chr6-146434424-T-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001278064.2(GRM1):āc.3213T>Cā(p.Pro1071=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00206 in 1,613,228 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. P1071P) has been classified as Benign.
Frequency
Consequence
NM_001278064.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRM1 | NM_001278064.2 | c.3213T>C | p.Pro1071= | synonymous_variant | 8/8 | ENST00000282753.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRM1 | ENST00000282753.6 | c.3213T>C | p.Pro1071= | synonymous_variant | 8/8 | 1 | NM_001278064.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00210 AC: 319AN: 152036Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00153 AC: 376AN: 245168Hom.: 0 AF XY: 0.00159 AC XY: 212AN XY: 133690
GnomAD4 exome AF: 0.00205 AC: 2999AN: 1461076Hom.: 2 Cov.: 54 AF XY: 0.00208 AC XY: 1510AN XY: 726820
GnomAD4 genome AF: 0.00209 AC: 318AN: 152152Hom.: 0 Cov.: 34 AF XY: 0.00175 AC XY: 130AN XY: 74354
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 17, 2021 | See Variant Classification Assertion Criteria. - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | GRM1: BP4, BP7 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Feb 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at